WASHINGTON — Defense Secretary Gates ousted the Air Force’s civilian and military chiefs yesterday, an unprecedented move that came after a classified Pentagon investigation found “a chain of failures” in the Air Force’s safeguarding of the American nuclear arsenal.

Gates decided to remove Air Force Secretary Michael Wynne and the chief of staff, General T. Michael “Buzz” Moseley, because “the focus of the Air Force leadership has drifted with respect to perhaps its most sensitive mission,” he said yesterday, adding that he would recommend replacements for both positions to President Bush shortly.

The departure of Messrs. Wynne and Moseley caps a disastrous period for the Air Force, one that has included a bomber wing inadvertently flying nuclear warheads over the continental United States, the mistaken and long-unnoticed transfer of secret nuclear-related materials to Taiwan, and a corrupt $50 million contract for a Thunderbirds air show that went to a company owned by a retired four-star general and a civilian friend of senior Air Force leaders.

Mr. Gates is the first defense secretary to fire both the military and civilian heads of a service at the same time, underscoring his willingness to shake up the Pentagon establishment to advance his priorities, officials said. Only a few months into his tenure, in March 2007, Mr. Gates forced Army Secretary Francis Harvey to resign over his handling of problems in care for wounded outpatient soldiers at Walter Reed Army Medical Center.

The recently completed Pentagon investigation into the Taiwan incident — in which four Air Force ballistic missile fuses were mistakenly shipped to Taiwan from the Defense Logistics Agency in 2006 — led M. Gates to realize that dramatic steps were needed to correct critical shortfalls in Air Force oversight of the nuclear arsenal. The classified materials were in Taiwan military control for about 17 months.

The investigation, led by Admiral Kirkland Donald, the Pentagon’s top official for nuclear safety, also found a “gradual erosion” of nuclear standards, technical expertise, and oversight over the past decade.

Speaking at a Pentagon news conference yesterday, Mr. Gates noted with some irritation that after the two highly publicized incidents in which the Air Force lost control over nuclear components, the call for a thorough investigation “was not initiated by the Air Force leadership, but required my intervention.”

The Taiwan shipment “represents a significant failure to ensure the security of sensitive military components,” Mr. Gates said. He added, “More troubling, it depicts a pattern of poor performance that was highlighted to us following last year’s incident involving the improper [transfer] of nuclear weapons between Minot Air Force Base and Barksdale Air Force Base.” In August, the service lost track of warheads for 36 hours when it unknowingly flew them between those bases, in North Dakota and Louisiana.

Not only did top officials fall short in those specific cases, Mr. Gates said, but “they failed to recognize systemic problems” or address them. He said a “substantial number” of Air Force generals and colonels also have been identified as “potentially subject to disciplinary measures.”